A three-dimensional model of a group II intron RNA and its interaction with the intron-encoded reverse transcriptase

Mol Cell. 2008 May 23;30(4):472-85. doi: 10.1016/j.molcel.2008.04.001.

Abstract

Group II introns are self-splicing ribozymes believed to be the ancestors of spliceosomal introns. Many group II introns encode reverse transcriptases that promote both RNA splicing and intron mobility to new genomic sites. Here we used a circular permutation and crosslinking method to establish 16 intramolecular distance relationships within the mobile Lactococcus lactis Ll.LtrB-DeltaORF intron. Using these new constraints together with 13 established tertiary interactions and eight published crosslinks, we modeled a complete three-dimensional structure of the intron. We also used the circular permutation strategy to map RNA-protein interaction sites through fluorescence quenching and crosslinking assays. Our model provides a comprehensive structural framework for understanding the function of group II ribozymes, their natural structural variations, and the mechanisms by which the intron-encoded protein promotes RNA splicing and intron mobility. The model also suggests an arrangement of active site elements that may be conserved in the spliceosome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins* / chemistry
  • Bacterial Proteins* / genetics
  • Bacterial Proteins* / metabolism
  • Binding Sites
  • Cross-Linking Reagents / metabolism
  • Introns / genetics*
  • Models, Molecular*
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Phylogeny
  • Protein Conformation
  • RNA Splicing
  • RNA* / chemistry
  • RNA* / genetics
  • RNA, Catalytic / chemistry
  • RNA, Catalytic / genetics
  • RNA, Catalytic / metabolism
  • RNA-Directed DNA Polymerase* / chemistry
  • RNA-Directed DNA Polymerase* / genetics
  • RNA-Directed DNA Polymerase* / metabolism

Substances

  • Bacterial Proteins
  • Cross-Linking Reagents
  • RNA, Catalytic
  • RNA
  • LtrA protein, Lactococcus lactis
  • RNA-Directed DNA Polymerase